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FFPE Human Pancreatic Ductal Adenocarcinoma Data with Human Immuno-Oncology Profiling Panel

In Situ Gene Expression dataset analyzed using Xenium Onboard Analysis 2.0.0

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Xenium In Situ Gene Expression data for human pancreatic ductal adenocarcinoma tissue using the Xenium Human Immuno-Oncology Profiling Panel with custom add-on.

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Interactively explore data with Xenium Explorer by downloading the Xenium Output Bundle (or Xenium Explorer subset) file. The subset bundle contains the experiment.xenium, gene_panel.json, morphology_focus/ directory of multi-file OME-TIFF files, analysis_summary.html,,,, and files.

See the Getting Started with Xenium Explorer page for more details. Follow these instructions to view the post-Xenium H&E image or image alignment file in Xenium Explorer.


FFPE-preserved tissues were purchased from Avaden Biosciences (Pancreatic Ductal Adenocarcinoma; Stage IIB; Grade 3).

Tissue preparation

Tissues were prepared following the Demonstrated Protocols Xenium In Situ for FFPE - Tissue Preparation Guide (CG000578) and Xenium In Situ for FFPE Tissues – Deparaffinization & Decrosslinking (CG000580). Probe hybridization, washing, ligation, and amplification were performed following the Xenium In Situ Gene Expression User Guide (CG000582).

Post-instrument processing followed the Demonstrated Protocol Xenium In Situ Gene Expression - Post-Xenium Analyzer H&E Staining (CG000613).

Gene panels

The Xenium Human Immuno-Oncology Profiling Panel (380 genes) was pre-designed by 10x Genomics. Genes were selected by a combination of data mining and manual curation (including literature review and domain expert feedback) and subsequent panel design was informed using single cell RNA sequencing data curated by the Tabula Sapiens cell atlas. Genes were chosen to allow identification of major immune cell types and subtypes, along with the inclusion of immune checkpoint molecules. This design enables delving deep into the cellular and subcellular levels of the tumor microenvironment, providing unparalleled insights into the behavior of both tumor and immune cells.

Xenium Analyzer

The instrument run was performed following the Xenium Analyzer User Guide (CG000584). The on-instrument analysis was run with Xenium Onboard Analysis version 2.0.0.

MetricDuctal adenocarcinoma
Median transcripts per cell41
Cells detected235,099
Nuclear transcripts per 100 µm²88.5
High quality decoded transcripts detected17,288,420
Region area (µm²)43,701,048

This dataset is licensed under the Creative Commons Attribution license.